glycosylation
Manual
This is the manual for GLYCOSYLATION, a program to be used in conjunction with SASREF for rigid body modeling of glycosylated structures. Glycan groups are added onto PDB structures for improved modeling against experimental scattering data of glycosylated proteins.
Introduction
GLYCOSYLATION adds glycan groups to asparagine (ASN) or serine (SER) residues of protein structures. The glycan groups are selected from a database of 50 precomputed structures found on glycosylated proteins ranging from 320 to 6820 Da. The structures were generated using Sweet2 which models the 3D structure of saccharides. The program can be run automatically, where the residues and glycan structures are determined by the program, given the number of glycans to be added and the total molecular weight of the glycans. Alternatively, expert mode can be used to specify exactly which glycan goes to which residue. This mode offers no detection of buried residues. NOTE: Only ASN residues are considered in the automatic mode.
Running
Usage:
$ glycosylation [OPTIONS] <MODEL>
Here, the MODEL is the protein structure in PDB or mmCIF format to be glycosylated.
Command-Line Arguments and Options
GLYCOSYLATION recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.
| Short Option | Long Option | Default | Description |
|---|---|---|---|
| --seed=<INT> | Set the seed for the random number generator | ||
| -k | -keepASN | False | (optional) whether to keep the ASN residue from the glycan structure. This means there will be an additional amino acid residue to the corresponding protein residue. This is meant to be used for modeling the glycan as a separate rigid body. |
| -n | -nsugars<number of glycans> | N/A | The number of glycans to be added to the structure. |
| -m | -mw<total molecular weight> | N/A | The total molecular weight of the glycan groups to be added. |
| -e | -expert | N/A | Run in expert mode. NOTE: only the number of glycans needs to be specified at the command line, not the MW. |
| -o | --output=<FILE> | write output to FILE. The output format depends on the FILE extension, supported are PDB and mmCIF format. | |
| -v | -version | N/A | Print version information and exit. |
| -h | --help | N/A | Print a summary of arguments, options, and exit. |
Output files
The output file contains the atoms in PDB or mmCIF format with a new header. The header is formatted as follows:
Parent PDB file: <input pdb file>
Number of glycans requested: <number of glycans>
Total molecular weight requested: <total molecular weight>
Keep ASN residues from glycans <T or F>
Glycan ASN chain Glycan ID name MW
-----------------------------------------------------------
1 60G B 6 complex_5_1 1141.0
2 78 F 28 hm_6_1 1155.0
3 204B F 8 complex_6_2 1141.0
4 78 H 27 hm_5_2 992.9
Total molecular weight of glycans added: 4429.8
Examples
Automatic
Glycosylate 1XMN.pdb with 4 glycans about 1000 Da each.
$ glycosylation 1XMN.pdb gly_1XMN.pdb -n 4 -mw 4000
Glyco data successfully loaded.
input PDB FILE: 1XMN.pdb
output PDB FILE: gly_auto_1XMN.pdb
IGNORED 1XMN.pdb A (less than 5 residues)
Found ( 28 ) non-buried ASN residues out of ( 42 ) ASN residues.
Calculated approximately 1000.0000000000000 Daltons per glycosylation.
Found 7 glyco structures available for glycosylation.
CA ASN B 60G
Placing glycan complex_5_1 on residue CA ASN B 60G
CA ASN F 78
Placing glycan hm_6_1 on residue CA ASN F 78
CA ASN B 62
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN H 143
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN B 78
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN H 60G
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN B 95
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN F 60G
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN B 147D
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN F 204B
Placing glycan complex_6_2 on residue CA ASN F 204B
CA ASN B 159
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
CA ASN H 78
Placing glycan hm_5_2 on residue CA ASN H 78
Pdb file written: gly_1XMN.pdb
Expert
Glycosylate 1XMN.pdb with 4 glycans and run in expert mode.
$> glycosylation 1XMN.pdb gly_1XMN.pdb -n 4 -e
Entering expert mode.
Glyco data successfully loaded.
input PDB FILE: 1XMN.pdb
output PDB FILE: gly_1XMN.pdb
Found ( 105 ) non-buried ASN residues out of ( 105 ) ASN residues.
Choose from the following ASN and SER residues:
< 1> CA SER B 20
< 2> CA SER B 27
< 3> CA SER B 36A
< 4> CA SER B 45
< 5> CA SER B 48
< 6> CA ASN B 60G
< 7> CA ASN B 62
< 8> CA SER B 72
< 9> CA ASN B 78
< 10> CA SER B 83
< 11> CA ASN B 95
< 12> CA ASN B 98
< 13> CA SER B 115
< 14> CA SER B 129B
< 15> CA ASN B 143
.
.
.
<105> CA SER H 214
Enter residue choices one at a time:
6
7
37
51
For each of the chosen ASN residues, choose a
sugar by first giving molecular weight range
then selecting from the available structures.
Enter approximate MW (Da):
1000
Found 7 glyco structures available for glycosylation.
Structure < 1>
Molecular weight: 1141.0
Name:complex_5_1
A-D-MANP-(1-6)+
|
A-D-MANP-(1-3)-B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN
|
B-D-XYLP-(1-2)+
Structure < 2>
Molecular weight: 1141.0
Name:complex_6_2
A-D-MANP-(1-6)+
|
A-D-MANP-(1-3)-B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN
|
B-D-XYLP-(1-2)+
Structure < 3>
Molecular weight: 846.7
Name:hm_4_1
a-D-Manp-(1-3)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn
Structure < 4>
Molecular weight: 1008.9
Name:hm_5_1
A-D-MANP-(1-6)+
|
B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN
|
A-D-MANP-(1-3)+
Structure < 5>
Molecular weight: 992.9
Name:hm_5_2
a-L-Fucp-(1-6)+
|
b-D-GlcpNAc-(1-4)-Asn
|
a-D-Manp-(1-6)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+
Structure < 6>
Molecular weight: 1155.0
Name:hm_6_1
A-L-FUCP-(1-6)+
|
A-D-MANP-(1-6)+ B-D-GLCPNAC-(1-4)-ASN
| |
B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)+
|
A-D-MANP-(1-3)+
Structure < 7>
Molecular weight: 1171.0
Name:hm_6_2
A-D-MANP-(1-3)-A-D-MANP-(1-6)+
|
B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN
|
A-D-MANP-(1-3)+
Choose from the following structures:
1
Repeat selection process for other glycans…
Placing glycan complex_5_1 on residue CA ASN B 60G
Placing glycan complex_5_1 on residue CA ASN B 62
WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue.
Placing glycan complex_5_1 on residue CA ASN D 78
Placing glycan complex_5_1 on residue CA ASN D 204B
Pdb file written: gly_1XMN.pdb